Fig. 3

The gene groups unique to sub-clades according to pan-genome analysis with core genome phylogenetic tree (a). The top panel (b) shows a single representative nucleotide sequence inferred for each gene of the pangenome. The middle panel (c) displays presence (blue) or absence (white) of blocks relative to genes and contigs in the pan-genome and metadata on disease site and health region (LHD). Disease site is classified as respiratory (green), cutaneous (orange) and blood (purple). There were four LHD regions identified as LHD-1 (orange), LHD-2 (red), LHD-3 (yellow) and LHD-4 (purple). Unique gene groups found in defined sub-clades have been circled and numbered accordingly; gene group I (red) - transposable elements and other proteins found in sub-clade 1; gene group II (orange) - 11 genes containing transposons, unique outer membrane proteins and a phenazine biosynthesis protein (PhzF); gene group III (green) – genes unique to sub-clade 2 containing tetO; gene group IV - sul1, genes for a fimbrial subunit type 1, sulphur carrying protein (ThiS), inner membrane transporter protein (RhIA) and VRR-NUC domain; gene group IV (purple) – genes unique to sub-clade 6 containing sdpA and sdpB, an integrase, von Willebrand factor type A domain protein and a putative transposon Tn552, all shown to be part of a NRPS/ PKS module and another NRPS module containing homologs of mbtB, irtA and irtB. The image was prepared using Phandango [21]